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Yorodumi- PDB-6f9z: Lysozyme crystallized in presence of 5 mM ammonium sulphate at pH 4.5 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f9z | ||||||
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Title | Lysozyme crystallized in presence of 5 mM ammonium sulphate at pH 4.5 | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å | ||||||
Authors | Camara-Artigas, A. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Orthorhombic lysozyme crystallization at acidic pH values driven by phosphate binding. Authors: Plaza-Garrido, M. / Salinas-Garcia, M.C. / Camara-Artigas, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f9z.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f9z.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 6f9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/6f9z ftp://data.pdbj.org/pub/pdb/validation_reports/f9/6f9z | HTTPS FTP |
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-Related structure data
Related structure data | 6f1lC 6f1mC 6f1oC 6f1pC 6f1rC 6f9xC 6f9yC 6fa0C 4e3uS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14060.808 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.11 % / Mosaicity: 0.3 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 5 mM Ammonium Sulphate, 0.4 M Sodium Chloride, 0.1 M Sodium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 24, 2017 / Details: Compound Refractive Lens | |||||||||||||||||||||
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.2→19.72 Å / Num. obs: 37901 / % possible obs: 97.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 12.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.02 / Rrim(I) all: 0.041 / Net I/σ(I): 15.5 / Num. measured all: 146195 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.6 %
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4E3U Resolution: 1.2→19.719 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0.12 / Phase error: 17.89
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.76 Å2 / Biso mean: 17.5061 Å2 / Biso min: 9.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.2→19.719 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25
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